Fig. 2.

Venn diagram of the number of unique spectra (cutoff: protein probability 90%, minimum peptides 1, minimum peptide probability 95%) observed with the four different extraction protocols. The four main circles contain the numbers of unique spectra that were found using the respective protocol, while smaller circles display the set of spectra that were also detected with another protocol. The set of spectra that could be identified with all four approaches is given in the middle circle. Numbers derive from Venn-diagrams calculated with Scaffold (Scaffold 3.00, Proteome Software, Portland, OR, USA) (SDS, extraction with sodium dodecyl sulfate; WSP, extraction with SDS and Phenol with pre-purification according to Wang et al.; NaOH, extraction based on sodium hydroxide with further phenol purification; SP, extraction with SDS and phenol).